September 2023 - ChimeraX-users - RBVI Mailing Lists

How to activate the Extract button in Segment Map function?
by Bo Chen 25 Sep '23

25 Sep '23

Dear ChimeraX, I tried to use Segment Map to remove some portions of the cryoEM map, and extract the selected portion, but the extract button remains shaded. The only tab in the "other tools" row that appears to be activated is "Fit". I have the most recent version of ChimeraX installaed(Sept 19). Could you give me some hints how to activate the extract in "Other tools" under the "Shortcut options" in "Segment Map"? Thanks! Bo

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Changing mesh size to save as STL file
by Arthur Melo 25 Sep '23

25 Sep '23

Dear colleagues, Is there a way to refine or decimate a mesh of a map to save as an STL file? All the best, Arthur

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symmetrizing the model
by Dmitry Semchonok 22 Sep '23

22 Sep '23

Dear colleagues, A very quick question - what is the command to apply the symmetry to the 3D model? (please provide a usage example if possible). Will the soft generate the symmetrized model after this command application? I found the one for Chimera but not for ChimeraX. Many thanks. Sincerely, Dmitry

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Equivalents to sop split & mask?
by Oliver Clarke 21 Sep '23

21 Sep '23

Hi, Is there a direct equivalent to the command “sop split” in ChimeraX? In the documentation for the “surface” command, I can see that there is an option to split by color, but not to split into individually selectable blobs. We use this a lot in Chimera, as a quick way to make a starting point for a mask to use in refinement, so it would be great to have in ChimeraX too. Also, is there an equivalent to the “mask” command from Chimera? I can’t seem to find it but perhaps it has a different name? Cheers Oli

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Labels of selected residues even with their model name
by svle＠tiscali.it 21 Sep '23

21 Sep '23

Hi, I have used matchmaker with four loaded models to compare the side chains orientation of some selected residues. It is possible to label the selected residues even with the information of the model name they belong to? Thanks. Saverio

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Open and play volume series in ChimeraX
by Wout Oosterheert 20 Sep '23

20 Sep '23

Dear ChimeraX team, I’m currently trying to open a volume and play a volume series in ChimeraX. According to the website (https://www.cgl.ucsf.edu/chimerax/docs/user/trajectories.html), opening a volume series should work like this: “Volume data can be opened as a series with open, employing filename wildcard symbols or globbing as needed to specify multiple files in a single command”. This seems simple enough, I indeed can open the volumes as a group. However, when I then try to play the series using: vseries play #1 direction oscillate loop true, I get the error: no volume series specified. Could you explain to me how I can get my group of volumes recognized as a volume series? The vseries page (https://www.cgl.ucsf.edu/chimerax/docs/user/commands/vseries.html) is very elaborate, but I cannot find alternative options of opening my volumes as a series. I know how to do things in regular Chimera, but would prefer to stick with ChimeraX because I make all my other figures with it. Thank you very much in advance!! Best, Wout Wout Oosterheert, PhD Humboldt Postdoctoral Fellow Max Planck Institute of Molecular Physiology Otto-Hahn-Str. 11 44227 Dortmund, Germany Phone +49-(0)231-133-2357 Email: wout.oosterheert(a)mpi-dortmund.mpg.de<mailto:wout.oosterheert@mpi-dortmund.mpg.de>

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seq_rmsd and align command
by dng26＠mrc-mbu.cam.ac.uk 19 Sep '23

19 Sep '23

Hello, I have two PDB models I am comparing, but I am having some issues generating the seq_rmsd attribute across all of the chains in the superposition that I want. My current models (same protein, but different states and slightly altered built sequences) have chains A/B/C/D/E/F separated over two domains of A/B/C and D/E/F, for example. My problem is that domain D/E/F is much larger than the former and when I run a matchmaker command such as this: matchmaker #1/A/B/C/D/E/F to #2/A/B/C/D/E/F pairing ss show true I get the resulting superposition favoring the /D/E/F domain (larger RMSD values on A/B/C). This would be fine, however, I want to investigate RMSD variation in D/E/F relative to a fixed position of A/B/C. If I run the following command I only get pairwise RMSDs (seq_rmsd header) for the specified chains but lack those of the larger D/E/F domain as they are not included. matchmaker #1/A/B/C to #2/A/B/C pairing ss show true I look to Calculate the RMSD between paired residues of chains /A/B/C/D/E/F without moving the current structures (after ‘mmaker’ alignment to A/B/C) with the ‘align’ command but the ‘move’ option set to nothing: align #1/A/B/C/D/E/F toAtoms #2/A/B/C/D/E/F move nothing matchNumbering (or matchAtomNames also tested) true I believe the above is what I want with regards to superposition for the RMSD calculations, but the ‘align’ job does not appear to give a seq_rmsd header attribute once run, even though the log seems to suggest it does a pairwise residue alignment to calculate the RMSDs. (Possibly because it does not just look at the CA like matchmaker does?) Is there a way to generate seq_rmsd attributes from the ‘align’ command, or is there a way to have an equivalent ‘move nothing’ in ‘mmaker’? I am looking to use seq_rmsd information to color the model and I am using v1.6.1. Any help is much appreciated! Dan.

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Chimerax
by François Ferron 15 Sep '23

15 Sep '23

Hi I am making a figure using a pdb and a density map in chimeraX1.6.1. each time I do that I have coloured arrows representing an axis that is in the middle. how do I get rid of them. I am sure it is trivial but I just could not find the answers in the manual. thanks François -- François Ferron, Ph.D. francois.ferron(a)univ-amu.fr @F2erron@fediscience.org Laboratoire CNRS - UMR 7257 (AFMB) AFMB - POLYTECH Case 925 163, Av de Luminy 13288 Marseille Cedex 09 France & European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany ######################################### Success is not final, failure is not fatal; it's the courage to continue that counts.

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Request to Resolve the Issue of Modifying Surface Dot Size in ChimeraX
by 18802001045＠163.com 14 Sep '23

14 Sep '23

Dear ChimeraX Maintenance Team, I hope this email finds you well. I am writing to seek assistance regarding an issue I have encountered while working with protein models in ChimeraX. After performing MPL calculations on protein models, I have found that I am unable to modify the dot size of the resulting surface representation. In Chimera, this task was easily accomplished through the "Model Panel" by adjusting the "MSMS Model Attributes". However, I have not been able to find a similar option or command in ChimeraX. I would greatly appreciate it if you could provide guidance or suggest a solution to address this matter. Being able to adjust the dot size of the surface representation is crucial for my current research project, and I rely heavily on the functionalities provided by ChimeraX. Thank you very much for your attention to this matter. I look forward to your kind assistance and prompt response. Best regards, Zhuangwei Zhang, Ph.D. State Key Laboratory of Analytical Chemistry for Life Science, Collaborative Innovation Centre of Chemistry for Life Sciences School of Chemistry and Chemical Engineering Nanjing University E-mail: dg21240166(a)smail.nju.edu.cn

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Monitor distance angle and torsion angles along trajectoty
by CUNIASSE Philippe 14 Sep '23

14 Sep '23

Dear all, I am wondering if there is a mean in ChimeraX to monitor distances, angles and torsion angles along a MD trajectory. The ideal would be to export a vector containing the frame id (a number) and the value measured for the distance or torsion angle. At the moment I can only built a distance histogram (which is already very usefull) after having created a pseudobond. But doing this, you lose the time evolution along the trajectory. Thanks in advance for your help. Best regards. Philippe. ----------------------------------------------- Philippe Cuniasse, PhD/HDR. Institut de Biologie Integrative de la cellule. UMR 9198 CNRS-CEA-Univ Paris Sud Bat 144 CE-Saclay 91191 Gif-sur-Yvette Cedex France Tel: (33) 1 69 08 56 35 Fax: (33) 1 69 08 47 12 Email: philippe.cuniasse(a)cea.fr<mailto:philippe.cuniasse@cea.fr> Web: http://biodev.cea.fr/rasmot3d/ [signature_575242473][signature_2653780937][signature_3407707164] -----------------------------------------------

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ChimeraX-users September 2023